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One of the major differences is moisture retention, this can be either a good thing or a bad thing.

If you install a below ground system you are watering the plants roots directly. If you are watering above ground the water must penetrate the ground and then permeate to the roots. Because of this you will lose some of the water to drying. Below ground the water is not as susceptible to drying from the sun and sticks around longer so you have to water less. The mulch or dirt insulates the moisture so it cannot be evaporated as quickly.

If your soil drains well then a below ground watering system will likely be good. However, if your soil does not drain well I'd expect that if used improperly a below ground watering system could lead to roots rotting as the water pools and does not drain away and it can't evaporate quickly because of the insulation.

Basically it really depends on your drainage situation and now diligent you are willing to be about over watering.